IGVFDS1873QGHK

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS1873QGHK/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS1873QGHK",
    "aliases": [
        "charles-gersbach:measurement-set-crispra-region3-mouse-hl1-targeted-hicar-rep3"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002440/",
        "status": "released",
        "term_name": "Hi-C assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS1873QGHK](/measurement-sets/IGVFDS1873QGHK/) has sequence file(s): [IGVFFI0417PVXJ](/sequence-files/IGVFFI0417PVXJ/), [IGVFFI3699PKGX](/sequence-files/IGVFFI3699PKGX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS1873QGHK/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
            "title": "Charles Gersbach"
        },
        "title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
    },
    "control_for": [],
    "creation_timestamp": "2024-10-23T19:20:12.051132+00:00",
    "donors": [
        {
            "@id": "/rodent-donors/IGVFDO1434JYIN/",
            "accession": "IGVFDO1434JYIN",
            "aliases": [
                "charles-gersbach:mouse-donor-HL-1"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Mus musculus"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI0417PVXJ/",
            "accession": "IGVFFI0417PVXJ",
            "aliases": [
                "charles-gersbach:measurement-set-ccrispra-region3-mouse-hl1-targeted-hicar-rep3-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:57.633821+00:00",
            "file_format": "fastq",
            "file_size": 982908871,
            "href": "/sequence-files/IGVFFI0417PVXJ/@@download/IGVFFI0417PVXJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/14155f2b-4f4c-4bd9-a412-ec73d305385a/IGVFFI0417PVXJ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/fastq/crispra_mouse/crispra_hicar_mouse_fastq/HL_1_TA446_3_noET1_ds.ddd23fd62a0943278602f69ba9bcacfe/HL_1_TA446_3_noET1_S16_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3699PKGX/",
            "accession": "IGVFFI3699PKGX",
            "aliases": [
                "charles-gersbach:measurement-set-ccrispra-region3-mouse-hl1-targeted-hicar-rep3-R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-10-23T19:29:58.781219+00:00",
            "file_format": "fastq",
            "file_size": 1097719082,
            "href": "/sequence-files/IGVFFI3699PKGX/@@download/IGVFFI3699PKGX.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/10/23/56f48a90-6d09-4a49-b403-0b9d7ebe195b/IGVFFI3699PKGX.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "released",
            "submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/HiCAR/fastq/crispra_mouse/crispra_hicar_mouse_fastq/HL_1_TA446_3_noET1_ds.ddd23fd62a0943278602f69ba9bcacfe/HL_1_TA446_3_noET1_S16_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7268XYPD/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "preferred_assay_title": "HiCAR",
    "protocols": [
        "https://www.protocols.io/view/hicar-for-mouse-hl-1-cells-following-enhancer-pert-36wgqn2yygk5"
    ],
    "release_timestamp": "2024-12-13T19:43:28.254417+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM5017HPIL/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5017HPIL",
            "aliases": [
                "charles-gersbach:in-vitro-system-ccrispra-region3-mouse-hl1-targeted-hicar-rep3"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS8122GWMC/",
                    "accession": "IGVFDS8122GWMC",
                    "file_set_type": "guide library",
                    "status": "released",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in a genomic locus"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0022835/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "HL-1",
                    "term_name": "HL-1"
                }
            ],
            "status": "released",
            "summary": "HL-1 cell line, female, Mus musculus C57BL/6J transfected with a guide library",
            "taxa": "Mus musculus"
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
        "title": "Ruhi Rai"
    },
    "submitted_files_timestamp": "2024-10-23T19:29:57.633821+00:00",
    "summary": "CRISPR HiCAR integrating a guide (sgRNA) library targeting accessible genome regions in a genomic locus",
    "uuid": "74e834b9-314d-4c20-b57c-ec6e765d74c3"
}